Job ID = 6452601 SRX = SRX017851 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:54:45 prefetch.2.10.7: 1) Downloading 'SRR038286'... 2020-06-21T07:54:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:56:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:56:35 prefetch.2.10.7: 'SRR038286' is valid 2020-06-21T07:56:35 prefetch.2.10.7: 1) 'SRR038286' was downloaded successfully Read 9225154 spots for SRR038286/SRR038286.sra Written 9225154 spots for SRR038286/SRR038286.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:07 9225154 reads; of these: 9225154 (100.00%) were unpaired; of these: 6477782 (70.22%) aligned 0 times 2224657 (24.12%) aligned exactly 1 time 522715 (5.67%) aligned >1 times 29.78% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 528131 / 2747372 = 0.1922 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 16:59:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:14: 1000000 INFO @ Sun, 21 Jun 2020 16:59:19: 2000000 INFO @ Sun, 21 Jun 2020 16:59:21: #1 tag size is determined as 24 bps INFO @ Sun, 21 Jun 2020 16:59:21: #1 tag size = 24 INFO @ Sun, 21 Jun 2020 16:59:21: #1 total tags in treatment: 2219241 INFO @ Sun, 21 Jun 2020 16:59:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:59:21: #1 tags after filtering in treatment: 2218939 INFO @ Sun, 21 Jun 2020 16:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:21: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:21: #2 number of paired peaks: 6738 INFO @ Sun, 21 Jun 2020 16:59:21: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:21: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:21: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:21: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:21: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 16:59:21: #2 alternative fragment length(s) may be 3,115 bps INFO @ Sun, 21 Jun 2020 16:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.05_model.r INFO @ Sun, 21 Jun 2020 16:59:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.05_summits.bed INFO @ Sun, 21 Jun 2020 16:59:30: Done! pass1 - making usageList (55 chroms): 0 millis pass2 - checking and writing primary data (849 records, 4 fields): 5 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 16:59:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 16:59:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:44: 1000000 INFO @ Sun, 21 Jun 2020 16:59:50: 2000000 INFO @ Sun, 21 Jun 2020 16:59:51: #1 tag size is determined as 24 bps INFO @ Sun, 21 Jun 2020 16:59:51: #1 tag size = 24 INFO @ Sun, 21 Jun 2020 16:59:51: #1 total tags in treatment: 2219241 INFO @ Sun, 21 Jun 2020 16:59:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:59:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:59:52: #1 tags after filtering in treatment: 2218939 INFO @ Sun, 21 Jun 2020 16:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:59:52: #1 finished! INFO @ Sun, 21 Jun 2020 16:59:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:59:52: #2 number of paired peaks: 6738 INFO @ Sun, 21 Jun 2020 16:59:52: start model_add_line... INFO @ Sun, 21 Jun 2020 16:59:52: start X-correlation... INFO @ Sun, 21 Jun 2020 16:59:52: end of X-cor INFO @ Sun, 21 Jun 2020 16:59:52: #2 finished! INFO @ Sun, 21 Jun 2020 16:59:52: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 16:59:52: #2 alternative fragment length(s) may be 3,115 bps INFO @ Sun, 21 Jun 2020 16:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.10_model.r INFO @ Sun, 21 Jun 2020 16:59:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.10_summits.bed INFO @ Sun, 21 Jun 2020 17:00:01: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (90 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:00:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:00:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:14: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:00:21: 2000000 INFO @ Sun, 21 Jun 2020 17:00:22: #1 tag size is determined as 24 bps INFO @ Sun, 21 Jun 2020 17:00:22: #1 tag size = 24 INFO @ Sun, 21 Jun 2020 17:00:22: #1 total tags in treatment: 2219241 INFO @ Sun, 21 Jun 2020 17:00:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:00:22: #1 tags after filtering in treatment: 2218939 INFO @ Sun, 21 Jun 2020 17:00:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:23: #2 number of paired peaks: 6738 INFO @ Sun, 21 Jun 2020 17:00:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:23: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 17:00:23: #2 alternative fragment length(s) may be 3,115 bps INFO @ Sun, 21 Jun 2020 17:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.20_model.r INFO @ Sun, 21 Jun 2020 17:00:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:00:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017851/SRX017851.20_summits.bed INFO @ Sun, 21 Jun 2020 17:00:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling